Articles
COST OF AFLP-BASED-FINGERPRINTING FOR PHYLO-GENETIC AND GENETIC-LINKAGE ANALYSES FOR THE PURPLE CONEFLOWER, AND SEVERAL ST. JOHN’S WORT AND GOLDENSEAL ACCESSIONS
Article number
756_9
Pages
85 – 94
Language
English
Abstract
DNA fragment analysis, known as DNA-fingerprinting, is extensively used in molecular genetics for finding linkage mapping distances and determining the evolutionary relationships among organisms.
These molecular genetics analyses heavily depend on computer hardware and software, i.e., bioinformatics tools.
In this study, Echinacea purpurea Magnus (purple coneflower), nine accessions of goldenseal (Hydrastis Canadensis) and 11 accessions of St.
Johns Wort (Hypericum spp.) were analyzed by amplified fragment length polymorphism (AFLP) based genetic markers.
An automated DNA analyzer (Global IR2 DNA Analyzer and Sequencer, Li-Cor Inc., Lincoln, NE, USA) was used to detect AFLP generated DNA-fragments The resulting digitized gel-images were scored for DNA-markers using the SagaMX Generation 2 version 3.1 software (Li-Cor Inc., Lincoln, NE, USA). The data for markers obtained from AFLP assays on coneflower leaf and pollen samples were acquired in JoinMap® 3.0 (Plant Research International, Wageningen, Netherlands) software for constructing genetic maps.
The goldenseal and St.
Johns Wort AFLP markers data were imported into the TreeCon-Dendogram (Scanalytics Inc., Fairfax, VA, USA) software to graph their genetic distances.
Expenditures for conducting all these analyses that included cost involved for consumables, depreciation of equipment and overhead as well as man-hours required for each experimental step were incorporated in the cost analyses.
For comparison, the projected cost of conducting AFLP analysis using the Applied Biosystems (ABI) DNA analyzer (ABI/Hitachi Prism 3100-Avant Genetic Analyzer, ABI, Foster City, CA, USA) was also estimated.
Data generated through these studies have direct applications in marker-assisted breeding programs and these data also provide cost assessment to facilitate the use of AFLP markers by the nursery industry.
These molecular genetics analyses heavily depend on computer hardware and software, i.e., bioinformatics tools.
In this study, Echinacea purpurea Magnus (purple coneflower), nine accessions of goldenseal (Hydrastis Canadensis) and 11 accessions of St.
Johns Wort (Hypericum spp.) were analyzed by amplified fragment length polymorphism (AFLP) based genetic markers.
An automated DNA analyzer (Global IR2 DNA Analyzer and Sequencer, Li-Cor Inc., Lincoln, NE, USA) was used to detect AFLP generated DNA-fragments The resulting digitized gel-images were scored for DNA-markers using the SagaMX Generation 2 version 3.1 software (Li-Cor Inc., Lincoln, NE, USA). The data for markers obtained from AFLP assays on coneflower leaf and pollen samples were acquired in JoinMap® 3.0 (Plant Research International, Wageningen, Netherlands) software for constructing genetic maps.
The goldenseal and St.
Johns Wort AFLP markers data were imported into the TreeCon-Dendogram (Scanalytics Inc., Fairfax, VA, USA) software to graph their genetic distances.
Expenditures for conducting all these analyses that included cost involved for consumables, depreciation of equipment and overhead as well as man-hours required for each experimental step were incorporated in the cost analyses.
For comparison, the projected cost of conducting AFLP analysis using the Applied Biosystems (ABI) DNA analyzer (ABI/Hitachi Prism 3100-Avant Genetic Analyzer, ABI, Foster City, CA, USA) was also estimated.
Data generated through these studies have direct applications in marker-assisted breeding programs and these data also provide cost assessment to facilitate the use of AFLP markers by the nursery industry.
Authors
A.N. Aziz, R. Sauve, F. Tegegne
Keywords
DNA-fingerprinting, bioinformatics, Echinacea purpurea, Hydrastis canadensi, Hypericum spp., genetic marker, genetic distance
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